chr10-88657742-G-T

Variant names:

• chr10-88657742-G-T
• rs701826

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.291 in 150,996 control chromosomes in the GnomAD database, including 6,716 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6716 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.291 AC: 43955 AN: 150876 Hom.: 6712 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.300

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.291 AC: 43981 AN: 150996 Hom.: 6716 Cov.: 31 AF XY: 0.295 AC XY: 21723 AN XY: 73628

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.305

Alfa AF: 0.228 Hom.: 904

Bravo AF: 0.295

Asia WGS AF: 0.456 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs701826; hg19: chr10-90417499;